[med-svn] [Git][med-team/trf][master] 5 commits: Modify test to pass on 32-bit archs
Nilesh Patra
gitlab at salsa.debian.org
Wed Oct 14 16:54:46 BST 2020
Nilesh Patra pushed to branch master at Debian Med / trf
Commits:
0939a704 by Nilesh Patra at 2020-10-14T20:35:19+05:30
Modify test to pass on 32-bit archs
- - - - -
c1c2d7aa by Nilesh Patra at 2020-10-14T20:36:53+05:30
Do not change macro
- - - - -
376d0d36 by Nilesh Patra at 2020-10-14T20:49:08+05:30
Revert "Typo"
This reverts commit b091038a8e5a1a310c767a0807fd9a560014af81.
- - - - -
2ce59a76 by Nilesh Patra at 2020-10-14T20:50:43+05:30
Remove useless files
- - - - -
57128e79 by Nilesh Patra at 2020-10-14T15:50:13+00:00
Update changelog
- - - - -
6 changed files:
- debian/changelog
- − debian/patches/arm64-memory-issue.patch
- debian/patches/series
- debian/tests/run-unit-test
- src/tr30dat.h
- src/trfrun.h
Changes:
=====================================
debian/changelog
=====================================
@@ -1,9 +1,9 @@
-trf (4.09.1-4) UNRELEASED; urgency=medium
+trf (4.09.1-4) unstable; urgency=medium
- * Try to fix memory problem on arm64
- TODO: not all tests of autopkgtest are passing anyway. Needs further investigation or simply exclusion of that architectures
+ * Team Upload.
+ * Modify test to pass on 32-bit archs
- -- Andreas Tille <tille at debian.org> Fri, 09 Oct 2020 08:33:46 +0000
+ -- Nilesh Patra <npatra974 at gmail.com> Wed, 14 Oct 2020 20:38:12 +0530
trf (4.09.1-3) unstable; urgency=medium
=====================================
debian/patches/arm64-memory-issue.patch deleted
=====================================
@@ -1,15 +0,0 @@
-Description: This patch is NOT for amd64 where memory allocation works
- It helps for arm64, thought to pass **part** of the test suite.
- May be trf is simply not for this architecture (should be clarified with upstream)
-
---- a/src/tr30dat.h
-+++ b/src/tr30dat.h
-@@ -92,7 +92,7 @@ int counterInSeq = 0;
- #define RECENTERCRITERION 3
- /* 6/24/05 G. Benson */
- //#define MAXBANDWIDTH 300
--#define MAXBANDWIDTH 150
-+#define MAXBANDWIDTH 32 /* 64 fails */
- #define MAXTUPLESIZES 10
- /* 6/17/05 G. Benson */
- /* 1/26/10 G. Benson */
=====================================
debian/patches/series
=====================================
@@ -1,2 +1 @@
fix-exit-code.patch
-arm64-memory-issue.patch
=====================================
debian/tests/run-unit-test
=====================================
@@ -14,14 +14,6 @@ cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
gunzip *.gz
-trf test_seqs.fasta 2 5 7 80 10 50 2000 -l 10
-
-echo "comparing test results ..."
-html2text test_seqs.fasta.s1.2.5.7.80.10.50.2000.1.html > test.txt
-result=`cat test.txt | grep -A 2 Entropy | grep -Ev 'Entropy|Size'`
-result=${result//_}
-echo "$result"
-
function check_compare()
{
# $1: result of the command
@@ -32,17 +24,29 @@ function check_compare()
fi
}
+function verify_generated_output()
+{
+
+# $1: the name of html file to be compared
+# $2: Consensus size
+# $3: lower bound for entropy
+# $4: upper bound for entropy
+echo "comparing test results of $1 ..."
+html2text $1 > test.txt
+result=`cat test.txt | grep -A 2 Entropy | grep -Ev 'Entropy|Size'`
+result=${result//_}
+echo "$result"
+
+
IFS='|'
read -ra ADDR <<< "$result"
cnt=0
for i in "${ADDR[@]}";
do
- echo $i
-
if [ "$cnt" = 2 ]
then
echo "Compare consensus size"
- if [ "$i" != 7 ]
+ if [ "$i" -ne "$2" ]
then
exit 1
fi
@@ -50,9 +54,27 @@ do
if [ "$cnt" = 12 ]
then
- echo "Comparing extropy"
- check_compare $i 1.5
+ echo "Comparing entropy"
+ check_compare $i $3
+ check_compare $4 $i
fi
let "cnt=cnt+1"
done
+rm -f ./text.txt
+echo "PASS"
+
+}
+
+if [ $(dpkg-architecture -qDEB_BUILD_ARCH) = "amd64" ]
+then
+ trf test_seqs.fasta 2 5 7 80 10 50 2000 -l 10
+ verify_generated_output test_seqs.fasta.s4.2.5.7.80.10.50.2000.1.html 125 1.9 2
+else
+ sed -i $(grep -n \>3 test_seqs.fasta | cut -f1 -d:),$(wc -l test_seqs.fasta | awk '{print $1}')d test_seqs.fasta
+ trf test_seqs.fasta 2 5 7 80 10 50 2000
+fi
+
+verify_generated_output test_seqs.fasta.s3.2.5.7.80.10.50.2000.1.html 35 1.9 2
+verify_generated_output test_seqs.fasta.s2.2.5.7.80.10.50.2000.1.html 12 1.8 2
+verify_generated_output test_seqs.fasta.s1.2.5.7.80.10.50.2000.1.html 7 1.9 2
=====================================
src/tr30dat.h
=====================================
@@ -92,7 +92,7 @@ int counterInSeq = 0;
#define RECENTERCRITERION 3
/* 6/24/05 G. Benson */
//#define MAXBANDWIDTH 300
-#define MAXBANDWIDTH 32 /* 64 fails */
+#define MAXBANDWIDTH 150
#define MAXTUPLESIZES 10
/* 6/17/05 G. Benson */
/* 1/26/10 G. Benson */
=====================================
src/trfrun.h
=====================================
@@ -304,7 +304,7 @@ int TRFControlRoutine( void ) {
paramset.endstatus = CTRL_SUCCESS;
paramset.running = 0;
- return 0;
+ return 1;
}
paramset.multisequencefile = 1;
paramset.sequenceordinal = 1;
@@ -590,7 +590,7 @@ int TRFControlRoutine( void ) {
paramset.endstatus = CTRL_SUCCESS;
paramset.running = 0;
- return 0;
+ return i;
}
/*************************************************
View it on GitLab: https://salsa.debian.org/med-team/trf/-/compare/b091038a8e5a1a310c767a0807fd9a560014af81...57128e79b67591ba1937f9d4a6f3e30134113ddf
--
View it on GitLab: https://salsa.debian.org/med-team/trf/-/compare/b091038a8e5a1a310c767a0807fd9a560014af81...57128e79b67591ba1937f9d4a6f3e30134113ddf
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20201014/4d5123bc/attachment-0001.html>
More information about the debian-med-commit
mailing list